Extract drug names

Hi @t_klok,

this is one of the problems were i started with "hey that's easy" and it turned out to be a 15operator process. Maybe there is another way to do this? @sgenzer might find one . Anyway, my solution is attached.

You might want to link up with @SvenVanPoucke . He is a physician and our medical expert in the community.

Best,

Martin

<?xml version="1.0" encoding="UTF-8"?><process version="8.1.000">
  <context>
    <input/>
    <output/>
    <macros/>
  </context>
  <operator activated="true" class="process" compatibility="8.1.000" expanded="true" name="Process">
    <process expanded="true">
      <operator activated="true" class="subprocess" compatibility="8.1.000" expanded="true" height="82" name="Subprocess (2)" width="90" x="45" y="34">
        <process expanded="true">
          <operator activated="true" class="generate_data_user_specification" compatibility="8.1.000" expanded="true" height="68" name="Generate Data by User Specification (4)" width="90" x="45" y="34">
            <list key="attribute_values">
              <parameter key="text" value="&quot;This is a drug which includes mydrug&quot;"/>
            </list>
            <list key="set_additional_roles"/>
          </operator>
          <operator activated="true" class="generate_data_user_specification" compatibility="8.1.000" expanded="true" height="68" name="Generate Data by User Specification (5)" width="90" x="45" y="136">
            <list key="attribute_values">
              <parameter key="text" value="&quot;just a text&quot;"/>
            </list>
            <list key="set_additional_roles"/>
          </operator>
          <operator activated="true" class="generate_data_user_specification" compatibility="8.1.000" expanded="true" height="68" name="Generate Data by User Specification (6)" width="90" x="45" y="238">
            <list key="attribute_values">
              <parameter key="text" value="&quot;thirddrug in another text twice: thirddrug&quot;"/>
            </list>
            <list key="set_additional_roles"/>
          </operator>
          <operator activated="true" class="append" compatibility="8.1.000" expanded="true" height="124" name="Append (2)" width="90" x="179" y="85"/>
          <connect from_op="Generate Data by User Specification (4)" from_port="output" to_op="Append (2)" to_port="example set 1"/>
          <connect from_op="Generate Data by User Specification (5)" from_port="output" to_op="Append (2)" to_port="example set 2"/>
          <connect from_op="Generate Data by User Specification (6)" from_port="output" to_op="Append (2)" to_port="example set 3"/>
          <connect from_op="Append (2)" from_port="merged set" to_port="out 1"/>
          <portSpacing port="source_in 1" spacing="0"/>
          <portSpacing port="sink_out 1" spacing="0"/>
          <portSpacing port="sink_out 2" spacing="0"/>
        </process>
        <description align="center" color="transparent" colored="false" width="126">Dummy data for drug texts you can replace this with read excel</description>
      </operator>
      <operator activated="true" class="nominal_to_text" compatibility="8.1.000" expanded="true" height="82" name="Nominal to Text" width="90" x="179" y="34">
        <description align="center" color="transparent" colored="false" width="126">Att needs to be text to work with Process Documents</description>
      </operator>
      <operator activated="true" class="text:process_document_from_data" compatibility="8.1.000" expanded="true" height="82" name="Process Documents from Data" width="90" x="313" y="34">
        <parameter key="vector_creation" value="Term Occurrences"/>
        <list key="specify_weights"/>
        <process expanded="true">
          <operator activated="true" class="text:tokenize" compatibility="8.1.000" expanded="true" height="68" name="Tokenize" width="90" x="45" y="34"/>
          <operator activated="false" class="operator_toolbox:FilterTokensUsingExampleSet" compatibility="0.11.000-SNAPSHOT" expanded="true" height="82" name="Filter Tokens Using ExampleSet" width="90" x="380" y="238">
            <parameter key="attribute" value="drugname"/>
            <description align="center" color="transparent" colored="false" width="126">only use specifed drug names</description>
          </operator>
          <connect from_port="document" to_op="Tokenize" to_port="document"/>
          <connect from_op="Tokenize" from_port="document" to_port="document 1"/>
          <portSpacing port="source_document" spacing="0"/>
          <portSpacing port="sink_document 1" spacing="0"/>
          <portSpacing port="sink_document 2" spacing="0"/>
        </process>
        <description align="center" color="transparent" colored="false" width="126">Generate bag of words</description>
      </operator>
      <operator activated="true" class="subprocess" compatibility="8.1.000" expanded="true" height="82" name="Subprocess" width="90" x="447" y="136">
        <process expanded="true">
          <operator activated="true" class="generate_data_user_specification" compatibility="8.1.000" expanded="true" height="68" name="Generate Data by User Specification" width="90" x="45" y="34">
            <list key="attribute_values">
              <parameter key="drugname" value="&quot;mydrug&quot;"/>
            </list>
            <list key="set_additional_roles"/>
          </operator>
          <operator activated="true" class="generate_data_user_specification" compatibility="8.1.000" expanded="true" height="68" name="Generate Data by User Specification (2)" width="90" x="45" y="136">
            <list key="attribute_values">
              <parameter key="drugname" value="&quot;anotherdrug&quot;"/>
            </list>
            <list key="set_additional_roles"/>
          </operator>
          <operator activated="true" class="generate_data_user_specification" compatibility="8.1.000" expanded="true" height="68" name="Generate Data by User Specification (3)" width="90" x="45" y="238">
            <list key="attribute_values">
              <parameter key="drugname" value="&quot;thirddrug&quot;"/>
            </list>
            <list key="set_additional_roles"/>
          </operator>
          <operator activated="true" class="append" compatibility="8.1.000" expanded="true" height="124" name="Append" width="90" x="179" y="85"/>
          <connect from_op="Generate Data by User Specification" from_port="output" to_op="Append" to_port="example set 1"/>
          <connect from_op="Generate Data by User Specification (2)" from_port="output" to_op="Append" to_port="example set 2"/>
          <connect from_op="Generate Data by User Specification (3)" from_port="output" to_op="Append" to_port="example set 3"/>
          <connect from_op="Append" from_port="merged set" to_port="out 1"/>
          <portSpacing port="source_in 1" spacing="0"/>
          <portSpacing port="sink_out 1" spacing="0"/>
          <portSpacing port="sink_out 2" spacing="0"/>
        </process>
        <description align="center" color="transparent" colored="false" width="126">Dummy data for drug names. You can replace this with read excel</description>
      </operator>
      <operator activated="true" class="set_role" compatibility="8.1.000" expanded="true" height="82" name="Set Role" width="90" x="581" y="136">
        <parameter key="attribute_name" value="drugname"/>
        <parameter key="target_role" value="id"/>
        <list key="set_additional_roles"/>
        <description align="center" color="transparent" colored="false" width="126">id will become header in transpose</description>
      </operator>
      <operator activated="true" class="transpose" compatibility="8.1.000" expanded="true" height="82" name="Transpose" width="90" x="715" y="136"/>
      <operator activated="true" class="data_to_weights" compatibility="8.1.000" expanded="true" height="82" name="Data to Weights" width="90" x="849" y="136"/>
      <operator activated="true" class="select_by_weights" compatibility="8.1.000" expanded="true" height="103" name="Select by Weights" width="90" x="1031" y="34">
        <description align="center" color="transparent" colored="false" width="126">Only let attributes through which were present in the lower exa</description>
      </operator>
      <operator activated="true" class="aggregate" compatibility="8.1.000" expanded="true" height="82" name="Aggregate" width="90" x="1184" y="34">
        <parameter key="use_default_aggregation" value="true"/>
        <parameter key="default_aggregation_function" value="sum"/>
        <list key="aggregation_attributes"/>
      </operator>
      <connect from_op="Subprocess (2)" from_port="out 1" to_op="Nominal to Text" to_port="example set input"/>
      <connect from_op="Nominal to Text" from_port="example set output" to_op="Process Documents from Data" to_port="example set"/>
      <connect from_op="Process Documents from Data" from_port="example set" to_op="Select by Weights" to_port="example set input"/>
      <connect from_op="Subprocess" from_port="out 1" to_op="Set Role" to_port="example set input"/>
      <connect from_op="Set Role" from_port="example set output" to_op="Transpose" to_port="example set input"/>
      <connect from_op="Transpose" from_port="example set output" to_op="Data to Weights" to_port="example set"/>
      <connect from_op="Data to Weights" from_port="weights" to_op="Select by Weights" to_port="weights"/>
      <connect from_op="Select by Weights" from_port="example set output" to_op="Aggregate" to_port="example set input"/>
      <connect from_op="Aggregate" from_port="example set output" to_port="result 1"/>
      <portSpacing port="source_input 1" spacing="0"/>
      <portSpacing port="sink_result 1" spacing="0"/>
      <portSpacing port="sink_result 2" spacing="0"/>
    </process>
  </operator>
</process>

Hi Martin,

Rapid(miner) answers..

Thx I think I understand.

But I would like to filter out drugnames using a list which contains the drugnames.
I do not want to enter all the reference drugnames by hand....

Hi,

sure you can just read in the Excel file instead of generating them by hand. That was just to generate some dummy data.

Best,

Martin

hi @t_klok - I'd want to see the data before really weighing in but just from what you describe I would use the Text Processing extension, tokenize, and then Filter Tokens (Dictionary) with the drug names. It's very similar to what @mschmitz built with his XML.

Scott

Hi each country provides a list with official drug names. Additionally, SNOMED can help you find drug names in a text. 

---

@sgenzer wrote:

hi @t_klok - I'd want to see the data before really weighing in but just from what you describe I would use the Text Processing extension, tokenize, and then Filter Tokens (Dictionary) with the drug names. It's very similar to what @mschmitz built with his XML.

Scott

 

---

Hi,

Please take a look at the technology Microsoft is testing: https://www.youtube.com/watch?v=c6exHAzNwy4#action=share

Cheers Sven

Thank you all.

I have a (large) list of drugnames and I want to see if freetext fields in an xcl contain any of these names.

So I query an xcl file with freetext cells and the reference is a file with all drugnames.

I do not want to enter all these drugnames one by one in rapidminer.